The game begins with Serge located in El Nido, a tropical archipelago inhabited by ancient natives, mainland colonists, and beings called Demi-humans. Serge slips into an alternate dimension in which he drowned on the beach ten years prior, and meets the thief, "Kid". As his adventure proceeds from here, Serge is able to recruit a multitude of allies to his cause. While assisting Kid in a heist at Viper Manor to steal the Frozen Flame, he learns that ten years before the present, the universe split into two dimensions—one in which Serge lived, and one in which he perished. Through Kid's Astral Amulet charm, Serge travels between the dimensions. At Fort Dragonia, with the use of a Dragonian artifact called the Dragon Tear, Lynx switches bodies with Serge. Unaware of the switch, Kid confides in Lynx, who stabs her as the real Serge helplessly watches. Lynx boasts of his victory and banishes Serge to a strange realm called the Temporal Vortex. He takes Kid under his wing, brainwashing her to believe the real Serge (in Lynx's body) is her enemy. Serge escapes with help from Harle, although his new body turns him into a stranger in his own world.
Players advance the game by controlling the protagonist Serge through the game's world, primarily by foot and boat. Navigation between areas is conducted via an overworld map, much like Chrono Trigger's, depicting the landscape from a scaled-down overhead view. Around the island world are villages, outdoor areas, and dungeons, through which the player moves in three dimensions. Locations such as cities and forests are represented by more realistically scaled field maps, in which players can converse with locals to procure items and services, solve puzzles and challenges, or encounter enemies. Like Chrono Trigger, the game features no random encounters; enemies are openly visible on field maps or lie in wait to ambush the party. Touching the monster switches perspectives to a battle screen, in which players can physically attack, use "Elements", defend, or run away from the enemy. Battles are turn-based, allowing the player unlimited time to select an action from the available menu. For both the playable characters and the computer-controlled enemies, each attack reduces their number of hit points (a numerically based life bar), which can be restored through some Elements. When a playable character loses all hit points, he or she faints. If all the player's characters fall in battle, the game ends and must be restored from a previously saved chapter—except for specific storyline-related battles that allow the player to lose. Chrono Cross's developers aimed to break new ground in the genre, and the game features several innovations. For example, players can run away from all conflicts, including boss fights and the final battle.
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